All functions

DEGSet() DEGSet() as.DEGSet()

DEGSet

DEGreport-package

Deprecated functions in package DEGreport

createReport()

Create report of RNAseq DEG anlaysis

deg()

Method to get all table stored for an specific comparison

degCheckFactors()

Distribution of gene ratios used to calculate Size Factors.

degColors()

Make nice colors for metadata

degComps()

Automatize the use of results() for multiple comparisons

degCorCov()

Calculate the correlation relationshipt among all covariates in the metadata table

degCovariates()

Find correlation between pcs and covariates

degDefault() degCorrect()

Method to get the default table to use.

degFilter()

Filter genes by group

degMA()

MA-plot from base means and log fold changes

degMB()

Distribution of expression of DE genes compared to the background

degMDS()

Plot MDS from normalized count data

degMV()

Correlation of the standard desviation and the mean of the abundance of a set of genes.

degMean()

Distribution of pvalues by expression range

degMerge()

Integrate data comming from degPattern into one data object

degObj()

Create a deg object that can be used to plot expression values at shiny server:runGist(9930881)

degPCA()

smart PCA from count matrix data

degPatterns()

Make groups of genes using expression profile.

degPlot()

Plot top genes allowing more variables to color and shape points

degPlotCluster()

Plot clusters from degPattern function output

degPlotWide()

Plot selected genes on a wide format

degQC()

Plot main figures showing p-values distribution and mean-variance correlation

degResults()

Complete report from DESeq2 analysis

degSignature()

Plot gene signature for each group and signature

degSummary()

Print Summary Statistics of Alpha Level Cutoffs

degVB()

Distribution of the standard desviation of DE genes compared to the background

degVar()

Distribution of pvalues by standard desviation range

degVolcano()

Create volcano plot from log2FC and adjusted pvalues data frame

geneInfo

data.frame with chromose information for each gene

geom_cor()

Add correlation and p-value to a ggplot2 plot

humanGender

DGEList object for DE genes betwen Male and Females

significants()

Method to get the significant genes